From 1f1acb921b6e45c73551dd647093138017c0db7f Mon Sep 17 00:00:00 2001
From: aheinri5 <Anna@netzkritzler.de>
Date: Fri, 18 Dec 2020 09:56:53 +0100
Subject: [PATCH] [docs] Updated documentation
---
man/OGS6.Rd | 16 ++++++++-
man/OGS6_Chain.Rd | 84 +++++++++++++++++++++++++++++++++++++++++++
man/OGS6_Ensemble.Rd | 34 +++++-------------
man/run_simulation.Rd | 4 +--
4 files changed, 110 insertions(+), 28 deletions(-)
create mode 100644 man/OGS6_Chain.Rd
diff --git a/man/OGS6.Rd b/man/OGS6.Rd
index 9db0425..f99e587 100644
--- a/man/OGS6.Rd
+++ b/man/OGS6.Rd
@@ -9,12 +9,14 @@ Constructor for the OGS6 base class
\section{Active bindings}{
\if{html}{\out{<div class="r6-active-bindings">}}
\describe{
-\item{\code{sim_name}}{Getter for OGS6 private parameter '.sim_name'}
+\item{\code{sim_name}}{Access to private parameter '.sim_name'}
\item{\code{sim_id}}{Getter for OGS6 private parameter '.sim_id'}
\item{\code{sim_path}}{Access to private parameter '.sim_path'}
+\item{\code{logfile}}{Access to private parameter '.logfile'}
+
\item{\code{ogs_bin_path}}{Getter for OGS6 private parameter '.ogs_bin_path'}
\item{\code{geometry}}{Getter for OGS6 private parameter '.geometry'}
@@ -68,6 +70,7 @@ Constructor for the OGS6 base class
\item \href{#method-add_vtkdiff}{\code{OGS6$add_vtkdiff()}}
\item \href{#method-add_insitu}{\code{OGS6$add_insitu()}}
\item \href{#method-get_status}{\code{OGS6$get_status()}}
+\item \href{#method-print_log}{\code{OGS6$print_log()}}
\item \href{#method-clear}{\code{OGS6$clear()}}
\item \href{#method-clone}{\code{OGS6$clone()}}
}
@@ -343,10 +346,21 @@ Adds a r2ogs6_insitu object
\subsection{Method \code{get_status()}}{
Checks if the OGS6 object has all necessary parameters for
starting a simulation
+print_log
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{OGS6$get_status()}\if{html}{\out{</div>}}
}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-print_log"></a>}}
+\if{latex}{\out{\hypertarget{method-print_log}{}}}
+\subsection{Method \code{print_log()}}{
+Prints logfile to console (if it exists)
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6$print_log()}\if{html}{\out{</div>}}
+}
+
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-clear"></a>}}
diff --git a/man/OGS6_Chain.Rd b/man/OGS6_Chain.Rd
new file mode 100644
index 0000000..c0c4bd5
--- /dev/null
+++ b/man/OGS6_Chain.Rd
@@ -0,0 +1,84 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ogs6_chain.R
+\name{OGS6_Chain}
+\alias{OGS6_Chain}
+\title{OGS6_Chain}
+\description{
+Constructor for the OGS6_Chain base class
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{OGS6_Chain$new()}}
+\item \href{#method-run_simulation}{\code{OGS6_Chain$run_simulation()}}
+\item \href{#method-print_log}{\code{OGS6_Chain$print_log()}}
+\item \href{#method-clone}{\code{OGS6_Chain$clone()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-new"></a>}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
+\subsection{Method \code{new()}}{
+Creates new OGS6_Chain object
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_Chain$new(ogs6_obj, iter_n)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{ogs6_obj}}{OGS6: A simulation object.}
+
+\item{\code{iter_n}}{number: Number of iterations (length of the chain)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-run_simulation"></a>}}
+\if{latex}{\out{\hypertarget{method-run_simulation}{}}}
+\subsection{Method \code{run_simulation()}}{
+Runs the simulation. This calls r2ogs6::run_simulation() internally.
+For chains, output will be written to logfiles.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_Chain$run_simulation()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-print_log"></a>}}
+\if{latex}{\out{\hypertarget{method-print_log}{}}}
+\subsection{Method \code{print_log()}}{
+Reads in logfile of simulation and prints it to the console.
+This calls print_log internally. If no index is specified, this will
+print the logfile of the last object in the chain.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_Chain$print_log(index)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{index}}{number: chain index of a OGS6 object}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_Chain$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}
diff --git a/man/OGS6_Ensemble.Rd b/man/OGS6_Ensemble.Rd
index 55cfa5d..772713a 100644
--- a/man/OGS6_Ensemble.Rd
+++ b/man/OGS6_Ensemble.Rd
@@ -9,9 +9,7 @@ Constructor for the OGS6_Ensemble base class
\section{Active bindings}{
\if{html}{\out{<div class="r6-active-bindings">}}
\describe{
-\item{\code{parameters}}{Access to private parameter '.parameters'}
-
-\item{\code{sim_name}}{Getter for private parameter '.sim_name'}
+\item{\code{parameters}}{Getter for private parameter '.parameters'}
\item{\code{ens_path}}{Getter for private parameter '.ens_path'}
@@ -23,7 +21,6 @@ Constructor for the OGS6_Ensemble base class
\subsection{Public methods}{
\itemize{
\item \href{#method-new}{\code{OGS6_Ensemble$new()}}
-\item \href{#method-add_parameter}{\code{OGS6_Ensemble$add_parameter()}}
\item \href{#method-run_simulation}{\code{OGS6_Ensemble$run_simulation()}}
\item \href{#method-clone}{\code{OGS6_Ensemble$clone()}}
}
@@ -51,36 +48,23 @@ have the same length.}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_parameter"></a>}}
-\if{latex}{\out{\hypertarget{method-add_parameter}{}}}
-\subsection{Method \code{add_parameter()}}{
-Adds a parameter.
+\if{html}{\out{<a id="method-run_simulation"></a>}}
+\if{latex}{\out{\hypertarget{method-run_simulation}{}}}
+\subsection{Method \code{run_simulation()}}{
+Runs the simulation. This calls r2ogs6::run_simulation() internally.
+For ensembles, output will be written to logfiles.
\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$add_parameter(parameter)}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$run_simulation(parallel = FALSE)}\if{html}{\out{</div>}}
}
\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
-\item{\code{parameter}}{list, length == 2: The first element references an
-OGS6 parameter, the second one is a list or vector of values.
-To find out how many values you need to supply, call ensemble_size
-on this object.}
+\item{\code{parallel}}{flag: Should the function be run in parallel?
+This is implementented via the 'parallel' package.}
}
\if{html}{\out{</div>}}
}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-run_simulation"></a>}}
-\if{latex}{\out{\hypertarget{method-run_simulation}{}}}
-\subsection{Method \code{run_simulation()}}{
-Runs the simulation. This calls run_simulation() internally. For
-ensembles, logfiles will never be written to console. This function
-should be suited for parallelization.
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$run_simulation()}\if{html}{\out{</div>}}
-}
-
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-clone"></a>}}
diff --git a/man/run_simulation.Rd b/man/run_simulation.Rd
index f5eefb6..05865c4 100644
--- a/man/run_simulation.Rd
+++ b/man/run_simulation.Rd
@@ -4,12 +4,12 @@
\alias{run_simulation}
\title{run_simulation}
\usage{
-run_simulation(ogs6_obj, output_to_log_file = TRUE)
+run_simulation(ogs6_obj, write_logfile = TRUE)
}
\arguments{
\item{ogs6_obj}{OGS6: Simulation object}
-\item{output_to_log_file}{flag: Should output be written to a log file?}
+\item{write_logfile}{flag: Should output be written to a logfile?}
}
\description{
Calls OGS6 object validator functions, exports all necessary
--
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